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Kasia Kedzierska
I am a 2nd year DPhil Candidate at the University of Oxford, studying the chromatin organisation in endometrial cancer. As a bioifnormatician, I spend most of my time either in command line writing Bash/Awk scripts or doing data analysis in R/Python.
I like teaching and deeply believe in Open Science. I am the President of #NGSchool Society with which I’ve been organising Summer Schoools in Bioinformatics. During last year edition - #NGSchool2019: Machine Learning for Biomedicine we recorded and published some of the lectures. This year, during #NGSchool2020: Statistical Learning in Genomics and 5 year anniversary conference we plan to record many more.
Research Experience
DPhil Candidate
Church group @ Wellcome Centre for Human Genetics, Wedge group @ Big Data Institute
University of Oxford, UK
2022 - 2018
- PhD project: Functional and evolutionary characterisation of chromatin organisation in endometrial cancer
Visiting Graduate Student
Ratan group
University of Virginia, USA
2018 - 2017
- Developed SONiCS - a tool for genotyping short tandem repeats (STRs) profiled using capture assays.
- Worked on the Master thesis - Analysis of the mutational burden across gene sets in cancer.
Visiting Graduate Student
Pemberton group
University of Virginia, USA
2017 - 2016
- Worked on Epigenetic regulation in prostate cancer.
- Performed experiments and analyzed data from RNA-seq, ATAC-seq, and ChIP-seq assays.
Research Assistant
Zebrafish Developmental Genomics
IIMCB, Warsaw, Poland
2016 - 2015
- I worked on the project: Elucidating gene regulatory network of zebrafish heart development using genomics.
- I was responsible for both computational and experimental aspects of the project.
Education
DPhil. Candidate, Genomic Medicine and Statistics
Nuffield Department of Medicine, Brasenose College
University of Oxford, UK
2022 - 2018
- Functional and evolutionary characterisation of chromatin organisation in endometrial cancer
- Wellcome Trust Studentship
M. Sc. Eng., Biotechnology
Warsaw University of Technology
Warsaw, Poland
2018 - 2015
- Thesis: Analysis of the mutational burden across gene sets in cancer.
- Thesis awarded the title of the best Master thesis in Bioinformatics defended in 2018.
B. Sc. Eng., Biotechnology
Warsaw University of Technology
Warsaw, Poland
2015 - 2011
Publications
Dynamics of cardiomyocyte transcriptome and chromatin landscape demarcates key events of heart development
Genome Research
N/A
2019
- Regulation networks in heart developmnent in zebrafish.
Genomic analysis of DNA repair genes and androgen signaling in prostate cancer
BMC Cancer
N/A
2018
- DNA repair genes and androgen signalling in prostate cancer cell lines.
SONiCS: PCR stutter noise correction in genome-scale microsatellites
Bioinformatics
N/A
2018
- Tool for genotyping short tandem repeats (STRs) profiled using capture assays, github.com/kzkedzierska/sonics
Posters, and Talks
Analysis of the mutational burden across gene sets in cancer
Polish Bioinformatics Society Symposium
Cracow, Poland
2019
- Invited talk
Differential mutation analysis across gene sets in cancers
The Biology of Genomes 2018
Cold Spring Harbor, NY, USA
2018
- Poster
Epigenetic regulation of prostate cancer
Visiting Graduate Traineeship Program Grantees Symposium
Charlottesville, VA, USA
2017
- Talk
Awards and honours
Best Master Thesis in Bioinformatics
N/A
N/A
2019 - 2018
- The Best Master Thesis defended in 2018 in Poland.
- Analysis of the mutational burden across gene sets in cancer Masther thesis defended at the Warsaw University of Technology; code for the analyses can be accessed github.com/kzkedzierska/cancers
Visiting Graduate Traineeship Program
N/A
N/A
2017 - 2016
- The Visiting Research Graduate Traineeship Program offered 12-month research traineeships for outstanding, qualified students from the life sciences at selected institutions in the United States.
Grasz o Staz
N/A
N/A
2015
- “Grasz o Staz” competition is a national, prestigious and highly competitive (1:25 success rate) scholarship program in Poland organized by PwC.
Teaching Experience
Unsupervised learning, Introduction to Python
#NGSchool2019: Machine Learning for Biomedicine
N/A
2019
- Tutor for the Introduction to Python (3 h workshop) and for the Unsupervised learning (1,5 h lecture).
- Materials for the Introduction to Python are available on github
Introduction to R
Wellcome Centre for Human Genetics
N/A
2019
- 8 week course in Introduction to R, Data Manipulation, Data Visualisation and RNA-seq data analysis.
- Materials available on github/kzkedziersa/r_intro
ATAC-seq workshop
#NGSchool2017: Single-cell Sequencing
N/A
2017
- Invited speaker
- Materials for the course can be available on gitub
Attended Workshops, Summer Schools
Machine Learning Summer School
Imperial College London, University College Londn
London, United Kingdom
2019
- 12-day intensive course on a variety of topics in machine learning.
Grants
Visegrad Grant to organize #NGSchool2019
N/A
2019
- 23,500 EUR awarded towards organising #NGSchool2019 allowed to keep the cost of attenting the school to the minimum and record the lectures for broader access.
Non profit work
President
N/A
2021 - 2018
- The goal of the Society is to promote and support science, with emphasis on computational biology.
- President since 2019; Vice President 2018 - 2019
President
Warsaw Society of Biotechnology
N/A
2016 - 2015
- Symbioza’s aim is to integrate the biotechnology environment in Poland starting from the youngest generations, and promotion and popularization of biotechnology.